[English] 日本語
Yorodumi
- PDB-4uc4: Crystal structure of hybrid tudor domain of human lysine demethyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uc4
TitleCrystal structure of hybrid tudor domain of human lysine demethylase KDM4B
ComponentsLysine-specific demethylase 4B
KeywordsREPLICATION / chromatin / tudor
Function / homology
Function and homology information


histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / brain development / HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression ...histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / brain development / HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression / chromatin remodeling / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain ...: / Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5612 Å
AuthorsWang, F. / Su, Z. / Denu, J.M. / Phillips Jr., G.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098248 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM059785-15/P250VA United States
CitationJournal: Nat Commun / Year: 2016
Title: Reader domain specificity and lysine demethylase-4 family function.
Authors: Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / ...Authors: Su, Z. / Wang, F. / Lee, J.H. / Stephens, K.E. / Papazyan, R. / Voronina, E. / Krautkramer, K.A. / Raman, A. / Thorpe, J.J. / Boersma, M.D. / Kuznetsov, V.I. / Miller, M.D. / Taverna, S.D. / Phillips, G.N. / Denu, J.M.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4B
B: Lysine-specific demethylase 4B


Theoretical massNumber of molelcules
Total (without water)26,7502
Polymers26,7502
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-4 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.436, 77.436, 50.758
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid UNK

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segid UNKB0

-
Components

#1: Protein Lysine-specific demethylase 4B / JmjC domain-containing histone demethylation protein 3B / Jumonji domain-containing protein 2B


Mass: 13374.822 Da / Num. of mol.: 2 / Fragment: Tudor domain (UNP 917-1031)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4B, JHDM3B, JMJD2B, KIAA0876 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: O94953, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06M Divalents (MgCl2/CaCl2), 0.1M Buffer pH8.5 (TRIS/Bicine) and 30% w/v EDO/P8K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 10956 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.83 Å2 / Rmerge(I) obs: 0.11 / Χ2: 0.474 / Net I/av σ(I): 8.366 / Net I/σ(I): 6.5 / Num. measured all: 71716
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
2.56-2.66.30.8135420.606
2.6-2.656.50.6625500.581
2.65-2.76.50.5945440.574
2.7-2.766.50.4855520.621
2.76-2.826.60.4035540.627
2.82-2.886.60.3535350.649
2.88-2.956.50.2975430.611
2.95-3.036.50.245540.611
3.03-3.126.60.1925450.622
3.12-3.226.60.1465580.605
3.22-3.346.50.1215510.548
3.34-3.476.60.1025260.489
3.47-3.636.60.0975630.48
3.63-3.826.60.0825490.371
3.82-4.066.60.0865490.383
4.06-4.376.60.0885430.246
4.37-4.816.60.0835530.262
4.81-5.516.60.0795570.209
5.51-6.926.60.0645330.195
6.92-306.50.065550.204

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GF7

2gf7


Resolution: 2.5612→27.977 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1177 10.76 %Random selection
Rwork0.1973 9762 --
obs0.2034 10939 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.44 Å2 / Biso mean: 48.0444 Å2 / Biso min: 22.43 Å2
Refinement stepCycle: final / Resolution: 2.5612→27.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 0 66 1782
Biso mean---44.72 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091748
X-RAY DIFFRACTIONf_angle_d1.1222370
X-RAY DIFFRACTIONf_chiral_restr0.044264
X-RAY DIFFRACTIONf_plane_restr0.005308
X-RAY DIFFRACTIONf_dihedral_angle_d14.294634
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A943X-RAY DIFFRACTION10.565TORSIONAL
12B943X-RAY DIFFRACTION10.565TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5612-2.67770.33681210.257612611382
2.6777-2.81880.32511810.24911781359
2.8188-2.99520.33371230.26212531376
2.9952-3.22610.30731860.240811701356
3.2261-3.55020.28071200.200412531373
3.5502-4.06260.23091720.178911911363
4.0626-5.11340.18451110.142412611372
5.1134-27.9790.22731630.200311951358
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1329-1.48360.15494.26391.64453.3813-0.1747-0.0671-0.4163-0.25820.39320.46230.0960.0492-0.17420.3731-0.0829-0.07090.29160.09520.3628.355949.884610.026
20.2414-0.3906-0.34026.25243.57631.9919-0.2551-0.17330.1966-0.40060.7513-0.6726-0.10260.4744-0.40350.4102-0.0192-0.0230.5047-0.00730.329536.646737.89562.2633
31.83330.8967-0.64192.63770.31930.7645-0.063-0.1202-0.17590.10790.2319-0.14030.22650.1456-0.16410.42980.0195-0.10620.29960.02180.314144.215648.40423.7397
44.42352.6156-1.68082.3249-0.66591.17610.2841-0.18030.06650.2392-0.10120.2491-0.0423-0.0364-0.12660.39920.0031-0.06230.34220.07760.392630.745143.080730.733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 918 through 949 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 950 through 1026 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 918 through 952 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 953 through 1026 )B0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more